This Github repository contains the code and data to used for in the published study: "Mutational signature in colorectal cancer caused by genotoxic pks+ E.coli", C. Pleguezuelos-Manzano, J. Puschhof and A. Rosendahl Huber et al.
https://www.nature.com/articles/s41586-020-2080-8 DOI: https://doi.org/10.1038/s41586-020-2080-8
For questions or suggestions: Please contact a.k.m.rosendahlhuber@prinsesmaximacentrum.nl
Please cite this paper when using this code for your research. BAM files containing the raw sequencing dat have been deposited at the European Genome-phenome Archive (https://ega-archive.org/) under the accesion code: EGAS00001003934.
SBS-pks and ID-pks signatures can be found in the folder Output.
Workflow: For the most easily deployment, unzip Genotoxic_Ecoli.zip folder. Set working directory in script #1 and execute R scripts following numbering 1-9. Dependencies: R version 3.6.0
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Load data and analyze single base substitution load
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Analysis of indels
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Transcriptional strand bias
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Wider single base substitution and indel context analysis
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Analyze data of second exposed organoid line
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Analysis of organoids exposed to recomplemented E.coli strain
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Presence of pks-patterns in > 1bp deletions
NOTE: scripts 8-9 use patient-level somatic variant and clinical data have been obtained from the Hartwig Medical Foundation under the data request number DR-084. Somatic variant and clinical data are freely available for academic use from the Hartwig Medical Foundation through standardized procedures. Privacy and publication policies, including co-authorship policies, can be retrieved from: https://www.hartwigmedicalfoundation.nl/en/data-policy/. Data request forms can be downloaded from https://www.hartwigmedicalfoundation.nl/en/applying-for-data/. To gain access to the data, this data request form should be emailed to info@hartwigmedicalfoundation.nl., upon which it will be evaluated within 6 weeks by the HMF Scientific Council and an independent Data Access Board. When access is granted, the requested data become available through a download link provided by HMF.
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SBS and indel refitting of mutational signatures in HMF data
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Presence of pks-motifs in > 1bp deletions and flanking bases in HMF data.